Question: Uniprot to KO
0
gravatar for lucie.semenec
11 weeks ago by
lucie.semenec0 wrote:

Hello,

I have used clusterProfiler to get Kegg entry names from uniprot IDs:

 keggID<-bitr_kegg(uniID, fromType='uniprot', toType='kegg', organism='abau')  which gives the resulting dataframe:
> str(keggID)
'data.frame':   1055 obs. of  2 variables:
 $ uniprot: chr  "A0A059ZNF8" "A0A0D8E944" "V5VFS9" "V5VH39" ...
 $ kegg   : chr  "IX87_00060" "IX87_00090" "IX87_00345" "IX87_00350" ...

and where uniID looks like:

> str(uniID)
 chr [1:3862] "A0A059ZTB3" "V5V7W3" "A0A0C0B3P7" "A0A0D5YCW0" "A0A059ZT40" "V5V8D0" "A0A0D5YC24" "A0A059ZJ30"

However, I would like to use the reconstruct pathway tool in KEGG mapper (https://www.kegg.jp/kegg/tool/map_pathway.html) but it requires a gene list KO annotation file where each gene has a corresponding K number instead of kegg entry name. For example:

gene1   K02874
gene4   K00416
gene7   K12864
gene10  K03695

Is there any way to get the "K" numbers from the Kegg entry names bitr_kegg() function gave me (ie. IX87_00060) or from uniprot names?

Thanks very much in advance!

clusterprofiler • 140 views
ADD COMMENTlink modified 11 weeks ago by genomax80k • written 11 weeks ago by lucie.semenec0
1
gravatar for genomax
11 weeks ago by
genomax80k
United States
genomax80k wrote:

Using KEGG API?

https://www.genome.jp/dbget-bin/get_linkdb?-t+genes+up:A0A059ZTB3
https://www.genome.jp/dbget-bin/get_linkdb?-t+genes+up:V5V7W3
ADD COMMENTlink written 11 weeks ago by genomax80k
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